User:Chinmay Shukla

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Chinmay Shukla

<html><b>Chinmay Shukla</b></html> <html><br></html> 352 Godavari Hostel, Indian Institute of Technology, Madras, Tamilnadu, India. <html><br>Email:<a href=""></a></html> <html><br>Email:<a href=""></a><br></html>


<html> <ul> <li><b>Master of technology in Biotechnology, <a href="">IIT Madras </a> (2013)<br> Bachelor of technology in Biotechnology, <a href="">IIT Madras </a> (2012)</b></li> Branch ranking – 1st<br> <li><b>Board of Higher Secondary Education (2008)<br> School: St. Xaviers Loyola Hall </b></li> Graduated with 86.1%<br> <li><b>Board of Secondary Education (2006)<br> School: St. Xaviers Loyola Hall </b></li> Graduated with 93.6% </ul> </html>

Research Projects

<html> <ul> <li><b>Khorana Scholar 2012: Metabolic Networks and DNA Computing</b></li> [<a href=""> Dr.Aseem Ansari </a>,<a href=""> Dr. Parmeswaran Ramanathan </a>, <a href=""> Dr. Jennifer Reed </a>; University of Wisconsin, Madison, May 2012 - July 2012] <br> <ol type:"i"> <li><b>Modeling and Regulating Metabolic Networks Using Gene Switches</b></li> <p><b>Abstract: </b>Metabolic engineering has helped produce synthetic anti malarial drugs, bio-fuels and important chemical molecules. Traditional approaches have used deletions or over expression of genes for engineering networks. These are static changes which can’t be reversed. We describe a novel method for dynamic regulation of metabolic networks. For demonstration, we identified key nodes (genes) in branched chain amino acid synthesis (BCAA) network which can be perturbed to increase the production of L-valine by 400% <i>in silico</i>. Valine is a commercially important small molecule by itself and also useful in the bio-fuels industry. We also integrated our model in a computational reconstruction of the cell (COBRA) to determine the global effects of our perturbations. To implement these perturbations <i>in vivo</i>, we are designing gene regulatory switches (TALEs) to modulate the activities of the key genes and control valine production. This method can be easily applied to control any gene or metabolic network.</p> <li><b>Constructing a Clock, NAND Gate and hence large scale circuits like memory, flip flops with simple DNA gate motif architecture which uses toehold mediated strand displacement reactions</b></li> <p><b>Abstract: </b>It is very advantageous to program molecular systems to perform complex autonomous tasks and this has motivated research into the design of synthetic biochemical circuits. Of late, cell-free nucleic acid systems have evolved that exploit non-covalent hybridization of toeholds and subsequent strand displacement reactions to create cascades that implement digital and analogue circuits. Recently, a simple DNA gate architecture has been described for synthesizing large scale circuits like comparators, square root circuit and pulse generators. Infact, a small DNA brain implementing the Hopfield network (with pre assigned weights) has also been made this way. Although AND and OR gates have been made but so far no one has been able to make the NOT gate and hence dual rail logic has to be used to convert all the gates in a circuit to AND/OR gates. Alongwith Devesh Bhimsaria, a graduate student in the <a href="">Ansari Lab</a>, I tried to make NAND gate (a universal gate) using a combination of a clock and a AND gate. </p> </ol> </ul> </html>

<html> <ul> <li><b>Studying the biogenesis of Primary Cilium - an important cell signalling organelle</b></li> [<a href="">Dr. Derek Toomre</a>, <a href=""> CINEMA Lab</a>, Yale University, May - July 2011] <br> <ol type:"i"> <li><b>Comparative Super-Resolution Imaging of the Primary Cilium</b></li> <p><b>Abstract: </b>Super Resolution microscopy is powerful technique to look at closely spaced objects. There are three major commercially available super resolution modalities – SIM, PALM and STED. There have been only a few studies giving a head to head comparison between various super resolution modalities. I directly compared these techniques to give more biological detail about a new and highly important organelle; the primary cilium. I showed that all the approaches can resolve changes in the axoneme ultra structure not visible by conventional confocal microscopy and that the cilium gets wider as we move from the tip to the base and hence it is more conical than cylindrical as traditionally thought of. I also used Total Internal Reflection Microscopy (TIRFM) to image the cilia in a novel way. In this way, I established and validated an ultra-sensitive microscopy approach to visualize the primary cilia. Based on my distinct findings, I am in the process of preparing the manuscript for a journal publication.</p> <li><b>Studying the biogenesis of the Primary Cilium</b></li> <p><b>Abstract: </b>Primary cilia are cellular organelles that localize to the apical surface of cells. Primary cilia membranes are rich in receptors and signaling proteins. One of the most common human genetic disorders, Autosomal Dominant Polycystic Kidney Disease (ADPKD), has been related to malfunction and/or changes in primary cilia formation caused by mutations in PKD1 or PKD2 genes. Due to the importance of the proteins encoded by these genes for the proper function of the primary cilium, researchers have been focused in understanding the mechanism that regulate primary cilium formation and proper targeting of membrane to these compartments. Spinning Disk Confocal Microscopy has been used to show that upon serum withdrawal Rab8 (a small GTPase involved in vesicular trafficking) assembles near the ciliary membrane in ~ 100min. The main focus of my experiments was to use TIRFM and show that Rab8 assembles near the ciliary membrane. This would help develop a primary cilia cell model analyzing the relation between vesicle fusion and the different stages of primary cilia formation. </p> </ul> </html> <html> <ul> <li><b>Functional studies of SNPs in the human renalase gene and their correlation with hypertension</b></li> [Dr. Nitish R Mahapatra, <a href=""> Cardiovascular Genetics Lab </a> , IIT Madras, August 2012 - April 2013] <p><b>Abstract:</b>The renalase protein is a flavin adenine dinucleotide-dependent amine oxidase. Renalase is secreted by the kidney and it degrades catecholamines like norepinephrine and dopamine which are circulating in the blood. Since, catecholamines cause general physiological changes that prepare the body for physical activity they lead to increase in heart rate, blood pressure and blood glucose levels. Hence, renalase which is known to degrade these molecules is also thought to have an effect on blood pressure. In the last few years, Single Nucleotide Polymorphisms (SNPs) have been identified in the Northern Han Chinese population and European populations which have a strong correlation with hypertension. Since, SNPs can vary in different populations, the first part of my project aims at examining whether SNPs in the renalase gene have a correlation with hypertension in Indian population also. If there is a correlation between the SNPs and hypertension, I will try to determine the effects of the SNP on renalase expression and hence find the molecular reasons for the correlation of the SNPs with hypertension. </p> </ul> </html> <html> Please feel free to <a href="">contact me</a> in case you want a more detailed report/poster for any of my research projects </html>

Industrial Experience

<html> <ul> <li><b>Pre Clinical Trials of a Pancreatic Cancer Vaccine and DNA Fingerprinting to find signature sequences in medicinal herbs</b></li> [<a href="">Cadila Pharmaceuticals</a>, Ahmedabad, May – July 2010] <p>I mainly worked in the Immunology department of Cadila Pharmaceuticals in the summer of 2010. I was involved in pre clinical trials for a pancreatic cancer vaccine. I used mice to test the vaccine for changes in the various immunological parameters like Interferon-gamma using ELISPOT Assay. I was also involved in doing DNA Fingerprinting studies to find unique/signature sequences in various plants/herbs known to have a medicinal value. For a brief time, I worked in the Quality Control Department of the company and did basic microbiology tests like finding total bacterial and fungal count in the stock samples of all the medications and nutritional supplements provided by the company.</p> </ul> </html>

Academic Projects

<html> <ul> <p> <li> I did a small project in the <a href="">Applied and Industrial Microbiology Laboratory</a> under <a href="">Dr. Sathyanarayana Gummadi</a> on characterizing a micro gravity reactor by doing mixing time studies and modeling cell growth and oxygen consumption profiles using computational fluid dynamics. A long term aim of the project was to culture mammalian cells in the reactor and study trans membrane proteins.</li> <li><b>Transcriptional Regulation of Retinoblastoma gene</b></li> [<a href="">Prof. S Mahalingam </a>, IIT Madras] <li><b>Photosynthesis: A Mathematical Model <a href="">(CFA Project) </a> </b></li> [<a href="">Prof. G K Suraishkumar </a>, IIT Madras] <li><b> Analyzing the transport Phenomenon in Leeches <a href="">(CFA Project) </a> </b></li> [<a href="">Prof. G K Suraishkumar </a>, IIT Madras] </p> </ul> Please feel free to <a href="">contact me</a> in case you want a more detailed report for any of these projects. </html>

Scholastic Achievements

<html><ul> <li>Consistently risen and currently at <b>Branch Position 1</b> in my class of 40 students.</li> <li><b>Khorana Scholar 2012:</b> Received a scholarship of $ 4500 through the DBT-Govt. of India, IUSSTF and UW-Madison to be among the top 30 students in India to undertake research at University of Wisconsin, Madison during May-July 2012.</li> <li>Awarded the <b>Dr. Anita Mehta-Damani Prize </b> for the best academic record in the 5th and 6th semesters in Biotechnology.</li> <li>Awarded the <b>Sri S Vishwanathan Prize </b> for securing the highest Cumulative Grade Point Average [CGPA] in Management minor of the B.Tech / Dual Degree / MA programme during 2010-2012.</li> <li>Secured a position in the <b>top 1% students in JEE 2008</b> (Joint Entrance Examination for IITs) written by over 300,000 students.</li> </ul></html>

Co-curricular & Extracurricular Activities

    <html> <li>Served the <a href="">TeNet group </a> for developing e learning software as a part of NSS, 2008-09.</li> <li>Head of <a href=""> Events, Biofest 2012 </a> the inaugural technical festival of Department of Biotechnology, IIT Madras.</li> <li>Captain and Member of the hostel <b>chess team.</b></li> </ul> </html>

    --Chinmay Shukla 11:27, 8 July 2012 (EDT)

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